library(dada2); packageVersion("dada2") # the dada2 pipeline
[1] ‘1.21.0’
library(ShortRead); packageVersion("ShortRead") # dada2 depends on this
[1] ‘1.52.0’
library(dplyr); packageVersion("dplyr") # for manipulating data
[1] ‘1.0.8’
library(tidyr); packageVersion("tidyr") # for creating the final graph at the end of the pipeline
[1] ‘1.2.0’
#library(Hmisc); packageVersion("Hmisc") # for creating the final graph at the end of the pipeline
library(ggplot2); packageVersion("ggplot2") # for creating the final graph at the end of the pipeline
[1] ‘3.3.5’
library(plotly); packageVersion("plotly") # enables creation of interactive graphs, especially helpful for quality plots
[1] ‘4.10.0’
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("UMI4Cats") # for demultiplexing in R
'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details
replacement repositories:
CRAN: https://cran.rstudio.com/
Bioconductor version 3.13 (BiocManager 1.30.16), R 4.1.1 (2021-08-10)
Warning: package(s) not installed when version(s) same as current; use `force = TRUE` to
re-install: 'UMI4Cats'
Old packages: 'RcppArmadillo'
Update all/some/none? [a/s/n]:
n
//Users/gordoncuster/Bioinformatics_software/idemp-master
preprocess.fp
[1] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess"
flags <- paste("-b", barcode.fp, "-I1", I1.fp, "-R1", R1.fp, "-R2", R2.fp, "-o", demultiplex.fp)
system2(idemp, args = flags)
barcode: /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/16S/testLopezUribe_BeeBread_Barcodes_16s.txt
Index reads: /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/16S/Undetermined_S0_L001_I1_001.fastq.gz
Read1 reads: /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/16S/Undetermined_S0_L001_R1_001.fastq.gz
Read2 reads: /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/16S/Undetermined_S0_L001_R2_001.fastq.gz
Output folder: /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed
GCTTATTGCTTAN Bel_CON3037_B
GACCATGTAGTAN Spr_CON3017_B
CTTCGCGGATGTN Sla_IPM2070_B
TGAGCGCACGCGN Dal_CF1051_B
CATGAGACTGTAN Sum_CF4005_B
TTACCCGCACAGN Bel_CF3045_A
AAGATTTGCAGCN Sla_CON2061_A
AACCGATGTACCN Ber_CF2006_A
GCCTTACGATAGN Dal_CON1057_A
ACGACCTACGCTN Bel_Control_A
ATGGCCTGACTAN Bel_CON3039_B
GCAAGCTGTCTCN Spr_CON3019_Be2
ATCACATTCTCCN Sla_IPM2071_B
CGAGTATACAACN Dal_CF1052_B
CCAGGGACTTCTN Sum_CF4006_B
ACAAGTGCTGCTN Bel_CF3047_A
CACTCTCCGGCAN Sla_CON2063_A
ATTAATGAAGCGN Ber_CF2007_A
ACCGATTAGGTAN Dal_CON1058_A
ATCGATCCACAGN Spr_Control_A
TCAATGACCGCAN Bel_IPM3042_B
TATCTTCCTGAAN Spr_IPM3023_B
AACGTCCTGTGCN Ber_IPM2001_B
TAAGCGTCTCGAN Dal_IPM1054_B
GAGGTATTCTGAN Sum_CON4010_B
CGTAAGATGCCTN Spr_CF3013_A
GGAGGGTACCGTN Sla_CF2065_A
TCAAGATCAAGAN Ber_CON2010_A
TGCAACTTGCAGN Sum_IPM4001_A
TACTAGATATTAN Sla_Control_A
CTTTATGTGTCAN Bel_IPM3044_B
GGTACTGTACCAN Spr_IPM3024_B
AAGGTGGACAAGN Ber_IPM2002_B
ACGCTCCCATCGN Dal_IPM1055_B
AGAGCTCCTCTGN Sum_CON4011_B
GCGTACGGGTGAN Spr_CF3016_A
AAGCGTACATTGN Sla_CF2066_A
CTGTTACAGCGAN Ber_CON2011_A
CCGAGTACAATCN Sum_IPM4002_A
GGTCTCCTACAGN Ber_Control_A
GGTCGAATTGCTN Bel_CF3045_B
TCAACTATGTCTN Sla_CON2061_B
TATAGAAGAATGN Ber_CF2006_B
CTAATATTTGAAN Dal_CON1057_B
GAGCATTACATGN Bel_CON3037_A
ATATACCTGCGGN Spr_CON3017_A
CAATATTCAATAN Sla_IPM2070_A
AAGTGCTTGGTAN Dal_CF1051_A
GCGGAGCACGTCN Sum_CF4005_A
TCCCGCCTACGCN Dal_Control_A
TTACCACATCTAN Bel_CF3047_B
TGGCATGTTGGTN Sla_CON2063_B
GTGTGCTAACGTN Ber_CF2007_B
TGAGTTCGGTCCN Dal_CON1058_B
AGACAAGCTTCCN Bel_CON3039_A
TATAATCCGAGGN Spr_CON3019_A
ATAAAGAGGAGGN Sla_IPM2071_A
AGTTTGCGAGATN Dal_CF1052_A
AAGCTAAAGCTAN Sum_CF4006_A
ACCCTGGGTATCN Sum_Control_A1
ATGCAACTCGAAN Spr_CF3013_B
ATCATCTCGGCGN Sla_CF2065_B
GTCTATACATATN Ber_CON2010_B
CTCAGGAGACTTN Sum_IPM4001_B
CATCCTGAGCAAN Bel_IPM3042_A
GTGACTAGTGATN Spr_IPM3023_A
TCATGTGAACGAN Ber_IPM2001_A
CACTTGCTCTCTN Dal_IPM1054_A
ACAATCCCGAGTN Sum_CON4010_A
GTTCCCAACGGTN Dilution
Water Aliquot
TTGGTGCCTGTGN Spr_CF3016_B
ATTGGGACATAAN Sla_CF2066_B
AGTTCGGCATTGN Ber_CON2011_Be2
TCTGATCGAGGTN Sum_IPM4002_B
GAATGACGTTTGN Bel_IPM3044_A
GAAGGAAAGTAGN Spr_IPM3024_A
AACTGGAACCCTN Ber_IPM2002_A
AGGAATACTCACN Dal_IPM1055_A
CCATCGACGCTCN Sum_CON4011_A
GTCACCAATCCGN NTC
barcodes: 81
Pairwise barcode edit distance:
0
7 0
8 8 0
10 8 7 0
7 7 6 8 0
8 8 7 5 9 0
8 8 9 7 8 9 0
9 5 8 8 7 8 6 0
6 6 7 8 8 7 9 8 0
8 7 8 6 8 8 6 6 7 0
8 6 8 8 5 7 8 8 7 6 0
7 7 8 8 7 9 7 7 9 7 7 0
7 8 9 8 7 8 7 6 9 6 7 7 0
8 8 10 7 8 9 6 7 7 7 8 7 8 0
8 8 7 7 6 10 9 8 9 7 7 6 8 7 0
7 7 8 7 6 9 6 7 9 5 7 5 6 8 5 0
8 7 8 8 7 8 7 8 7 6 7 8 8 7 9 7 0
8 7 8 6 8 7 6 7 8 7 8 9 7 8 9 6 8 0
6 4 8 9 7 9 7 6 6 6 7 9 8 8 9 8 7 7 0
9 8 9 6 8 6 6 6 7 6 7 9 6 7 9 8 7 6 7 0
8 7 9 6 6 8 8 8 8 7 7 7 7 8 6 5 5 5 7 6 0
7 7 8 8 6 8 8 9 7 8 6 9 8 9 10 8 5 8 8 6 7 0
8 7 7 8 7 9 6 6 8 5 7 7 7 9 8 6 6 8 7 6 8 6 0
8 7 7 5 6 7 7 7 9 8 7 5 7 8 7 7 7 8 8 8 6 6 6 0
5 7 10 7 6 10 6 9 8 8 7 7 7 6 6 8 7 9 7 8 9 6 6 6 0
7 8 7 8 6 9 8 8 8 7 8 5 7 7 7 6 9 6 9 8 8 9 8 8 8 0
9 8 8 5 7 8 8 8 9 7 9 7 10 6 6 7 9 8 8 9 7 9 8 6 6 6 0
9 7 9 7 7 7 7 8 8 8 9 7 8 6 8 7 7 7 6 6 5 7 9 5 7 8 8 0
7 7 9 7 7 7 6 9 7 8 8 6 8 8 8 7 8 8 8 7 7 7 8 7 8 6 8 6 0
7 5 8 10 6 8 8 7 7 8 7 7 8 7 8 8 8 8 6 8 7 7 8 7 7 8 10 5 8 0
5 6 7 10 6 8 8 8 7 9 8 7 7 8 9 8 6 6 7 8 7 8 7 7 7 6 10 9 8 7 0
7 6 9 7 8 7 8 7 8 7 6 6 8 6 8 8 7 6 9 8 7 8 7 8 7 6 5 9 7 6 6 0
10 8 9 7 8 7 6 7 8 8 6 8 10 6 8 8 9 8 9 6 9 9 8 7 7 9 7 7 8 8 9 8 0
9 9 8 7 9 7 7 8 6 6 8 7 7 8 8 8 6 8 8 5 8 8 6 7 9 8 8 9 8 9 9 9 7 0
9 8 9 5 7 7 7 9 8 5 7 6 7 8 7 6 8 9 8 5 9 7 5 6 5 7 7 9 7 8 10 8 7 5 0
5 7 6 8 7 9 9 9 6 8 8 8 10 9 9 8 8 9 7 9 8 9 6 8 6 7 7 9 8 8 6 6 9 8 8 0
8 7 8 6 7 7 7 7 6 6 7 7 8 7 7 8 9 8 8 6 9 8 5 5 6 9 6 8 8 7 10 9 5 5 5 6 0
7 9 7 7 6 8 7 9 7 8 7 9 9 6 8 8 6 7 7 7 6 7 8 8 7 6 8 7 7 8 6 7 8 7 9 6 7 0
8 8 8 7 6 9 7 6 7 6 9 7 9 4 6 7 9 8 6 7 8 10 8 9 8 8 7 6 9 7 9 8 7 6 7 8 5 7 0
8 8 8 8 9 6 8 9 6 8 7 9 8 7 10 9 6 9 10 5 9 6 8 9 7 8 7 9 6 9 9 5 7 6 5 8 8 8 9 0
6 8 7 7 7 10 8 7 8 7 8 7 7 9 7 7 9 8 7 8 8 8 8 9 7 6 7 9 6 8 8 7 8 8 9 7 7 9 8 7 0
8 7 8 7 8 9 9 6 8 5 8 5 6 8 6 5 7 7 7 9 6 8 7 7 7 6 9 7 5 7 6 7 10 8 7 8 8 9 7 9 6 0
9 8 7 8 6 7 8 7 8 9 7 8 9 8 9 9 10 6 8 7 8 8 9 7 8 7 9 6 8 5 9 9 7 9 8 9 6 9 6 9 8 8 0
7 7 9 10 6 9 6 9 9 9 9 8 7 6 8 8 7 8 7 9 7 5 9 7 6 7 10 7 7 6 5 8 9 10 9 8 9 7 9 9 8 7 7 0
6 5 9 6 8 7 6 7 5 8 7 7 8 5 8 8 9 8 6 6 9 7 8 8 5 8 7 8 6 8 9 7 6 6 6 8 4 7 6 6 7 8 7 8 0
8 9 8 8 7 6 6 9 9 6 6 7 7 8 9 7 7 6 9 6 7 6 6 7 8 7 9 9 6 8 7 8 9 7 6 7 8 6 9 6 8 8 7 7 8 0
6 6 9 10 6 9 7 9 7 8 8 7 8 5 8 8 6 7 7 8 7 7 8 7 6 7 9 4 8 6 7 8 8 8 8 9 7 7 6 8 9 6 7 4 6 9 0
7 7 9 8 6 10 7 7 8 7 5 8 9 9 7 5 6 9 5 9 8 7 6 6 7 9 8 8 8 7 8 7 7 8 7 6 7 8 9 9 7 9 9 7 8 7 7 0
7 7 8 6 6 9 8 7 8 6 8 6 9 7 6 8 9 9 6 8 8 10 8 8 8 7 6 7 9 9 9 8 7 7 7 6 7 8 5 9 8 7 9 10 6 9 9 8 0
10 8 7 6 9 6 9 6 8 5 7 7 7 7 8 8 7 10 7 7 7 8 6 6 9 10 8 7 7 8 10 8 10 6 8 9 9 8 7 6 8 7 9 10 9 7 10 9 7 0
7 6 7 7 7 5 10 7 9 7 6 8 6 8 7 9 8 8 7 8 7 7 8 6 8 8 9 7 7 5 8 7 10 7 6 9 7 6 8 9 8 6 7 7 8 7 8 8 8 7 0
7 6 7 8 9 9 7 8 8 8 7 7 8 9 8 7 9 8 7 9 8 7 8 7 7 7 7 8 6 8 8 7 10 9 8 8 8 9 9 9 6 7 9 7 7 8 9 6 8 8 9 0
8 8 6 6 8 8 8 9 8 6 6 7 10 8 8 7 9 7 8 8 9 8 8 7 7 7 5 8 8 9 9 6 8 7 8 7 8 6 8 6 6 8 8 10 7 7 9 6 6 7 8 7 0
8 9 8 6 7 8 7 8 7 8 8 7 6 7 8 7 7 8 7 9 7 8 6 7 8 8 7 8 8 9 8 6 8 8 6 6 8 8 6 8 8 6 9 9 8 9 8 7 7 9 8 6 8 0
8 8 9 8 8 8 7 6 9 7 8 4 5 8 7 6 9 8 8 8 8 9 6 8 8 6 8 9 6 7 8 7 10 7 7 9 8 9 8 8 7 8 7 9 8 7 9 8 8 8 7 7 9 7 0
9 8 8 8 8 6 7 9 8 8 8 9 8 8 11 8 7 6 9 6 7 5 7 7 7 8 9 6 7 7 8 9 9 7 7 9 8 7 8 7 9 8 6 7 7 5 7 8 9 8 8 8 9 8 9 0
10 8 7 7 8 8 7 7 8 9 9 9 9 9 9 7 10 5 8 8 8 9 9 8 10 7 9 6 8 8 9 9 7 10 9 8 8 8 9 10 10 8 5 7 8 5 9 9 9 9 9 9 9 9 8 5 0
8 8 6 8 9 8 5 9 6 8 7 9 10 7 10 7 7 7 8 8 9 7 8 8 7 8 8 8 8 9 7 8 7 8 9 7 8 7 8 6 8 9 8 8 8 8 7 7 9 10 9 8 6 8 9 7 8 0
6 6 9 7 7 9 7 7 7 6 6 7 8 7 8 7 7 7 6 8 8 8 8 7 6 7 8 6 8 6 9 8 6 7 6 7 5 5 8 9 7 7 7 8 7 8 7 6 9 9 6 8 7 9 7 8 8 8 0
8 6 8 10 8 8 7 5 7 7 7 7 8 9 7 8 7 9 6 9 9 9 7 9 10 9 8 10 9 7 7 8 7 6 8 8 8 10 7 9 9 7 9 10 8 9 9 7 8 6 9 9 9 8 7 9 8 7 8 0
8 7 9 8 5 8 8 8 8 6 6 8 6 9 9 7 8 7 7 6 7 6 9 5 7 9 8 6 4 8 8 8 8 7 7 8 7 6 9 8 8 7 8 6 8 6 8 7 7 8 6 7 8 8 7 7 7 8 6 9 0
9 7 7 6 8 7 6 8 8 6 7 8 6 9 9 6 5 6 6 5 6 6 6 7 8 8 10 8 6 10 7 9 8 6 6 8 8 7 10 7 8 6 9 7 7 5 8 7 8 8 8 7 8 6 8 5 7 8 8 8 5 0
6 6 8 10 8 8 9 9 4 8 8 8 7 5 8 8 8 8 7 5 7 7 9 10 7 8 8 7 8 6 7 6 8 8 9 8 7 7 6 6 7 6 7 7 6 8 6 8 8 9 6 8 6 9 8 8 9 6 7 8 8 8 0
7 8 6 8 5 8 10 8 8 9 7 7 7 7 4 7 9 8 8 8 8 10 9 8 8 6 7 7 9 7 7 9 8 10 9 8 8 8 6 9 8 7 6 8 8 9 9 10 6 8 7 9 7 9 8 9 7 7 8 7 9 8 7 0
8 6 7 9 7 7 8 7 8 7 5 7 8 7 10 8 5 7 7 7 7 6 6 8 9 7 9 7 7 8 6 6 7 8 9 7 8 6 8 7 9 8 8 7 7 7 7 7 9 8 7 9 8 9 9 8 7 8 6 6 7 7 8 6 0
7 7 8 8 7 8 8 9 7 6 7 7 8 8 8 7 9 8 7 8 8 7 8 8 7 7 7 9 7 6 8 7 9 9 8 5 8 6 7 7 6 6 7 6 7 8 8 7 8 9 8 6 5 8 7 8 7 7 7 8 6 7 6 7 8 0
8 7 7 6 5 7 7 8 8 8 7 7 8 7 8 7 8 6 8 8 4 7 9 6 7 8 7 4 7 7 6 7 6 8 9 7 9 5 8 9 9 7 6 8 8 8 7 8 7 6 7 7 6 8 10 8 7 8 7 8 7 6 8 6 5 8 0
7 8 7 8 7 8 8 7 7 6 7 6 6 8 6 5 6 9 9 8 7 7 6 7 7 7 9 9 8 6 6 8 8 7 6 9 8 8 8 9 8 6 9 9 8 8 7 7 8 8 8 8 7 7 6 10 11 7 8 6 8 7 7 7 7 8 8 0
9 7 6 8 8 8 7 8 8 6 7 7 8 9 8 5 6 7 7 5 6 7 6 8 8 9 8 6 7 9 9 9 8 6 7 8 9 8 8 8 9 7 9 8 8 6 7 7 8 8 9 8 8 8 9 4 6 6 8 8 6 6 7 8 6 8 8 8 0
9 8 6 7 8 6 9 10 7 6 8 9 8 9 10 10 8 8 8 8 9 9 10 9 9 9 7 9 9 9 9 8 9 6 8 8 9 7 9 5 6 8 9 10 8 6 10 9 8 7 7 8 4 9 10 8 9 6 8 9 8 8 7 8 8 6 8 9 7 0
13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 0
7 9 6 6 6 8 9 10 9 9 6 9 10 10 8 7 9 7 9 7 7 6 5 7 7 8 7 9 7 9 7 8 7 7 6 7 6 7 8 7 8 9 8 8 8 6 10 6 6 7 7 7 7 7 10 7 9 8 9 8 8 7 8 7 9 7 8 7 8 8 13 0
8 9 7 9 6 8 9 8 8 9 6 10 9 8 6 9 9 7 8 6 8 8 9 8 8 9 8 7 8 6 8 8 5 8 9 9 6 7 8 9 9 10 7 8 8 9 8 8 8 9 6 9 8 9 9 10 8 6 8 7 6 9 6 7 7 8 7 8 10 9 13 7 0
7 8 6 7 8 7 7 9 7 8 7 9 8 9 9 8 7 7 8 7 9 9 7 8 8 8 8 10 8 7 8 7 6 5 6 7 5 8 9 7 6 9 8 10 7 8 8 8 8 8 7 8 8 6 7 8 8 6 8 7 8 7 7 8 8 8 9 8 8 7 13 6 5 0
7 8 6 7 7 8 8 8 7 6 8 9 9 9 9 8 8 7 5 6 7 7 8 8 9 8 8 5 8 7 8 9 9 8 9 7 10 6 8 8 8 7 7 8 9 7 9 8 6 7 8 6 6 7 9 4 7 6 8 9 8 7 6 7 8 6 6 8 6 7 13 7 9 9 0
7 7 8 7 7 9 8 7 5 8 8 6 7 9 7 8 9 7 9 8 7 9 6 6 7 7 8 9 8 7 8 8 8 9 7 6 6 9 8 8 8 7 6 7 6 7 8 7 8 9 7 8 8 7 7 8 7 8 8 8 9 8 7 8 9 7 8 8 7 9 13 7 8 7 8 0
9 6 9 7 6 9 7 7 7 9 8 8 10 7 7 9 10 7 7 8 7 10 8 8 7 8 7 7 8 7 10 8 6 9 9 8 6 9 8 9 8 8 6 9 7 9 8 7 7 10 8 8 8 8 8 9 7 8 5 9 8 10 8 7 8 7 7 10 9 9 13 8 7 8 9 5 0
9 9 9 8 7 8 8 6 9 7 8 8 8 9 6 7 8 7 9 7 7 10 8 9 8 7 6 9 9 7 10 7 6 8 8 10 7 8 8 9 7 7 7 10 9 9 9 8 7 8 9 10 7 9 7 9 9 8 6 7 7 9 8 6 8 9 7 5 8 8 13 8 7 8 8 8 8 0
8 8 11 8 7 9 6 8 8 6 6 7 5 5 8 7 9 7 7 6 7 8 8 7 5 7 7 8 7 7 8 7 7 7 6 9 7 8 6 6 8 8 8 7 7 7 7 8 7 9 8 7 8 7 6 8 8 8 7 9 5 7 7 8 9 6 9 8 7 10 13 9 7 9 10 7 6 8 0
8 7 7 6 6 8 9 7 7 5 7 6 7 7 5 7 7 8 7 7 6 8 8 7 9 7 8 8 8 8 8 9 9 8 7 8 7 7 6 9 7 6 7 9 8 8 7 9 6 7 7 8 8 8 7 9 8 8 7 7 8 7 9 6 6 9 7 6 7 8 13 9 9 7 6 6 9 7 8 0
9 8 8 7 9 7 10 8 7 7 8 7 5 9 8 9 8 7 9 6 7 8 8 7 8 7 8 7 7 8 9 7 9 6 7 9 9 8 8 5 7 6 8 9 7 7 9 11 8 7 5 9 7 8 7 7 8 9 9 10 8 6 7 7 8 6 8 8 8 5 13 9 9 7 9 8 8 7 8 8 0
Closest barcodes, editDistance=4
ACCGATTAGGTAN:GACCATGTAGTAN
CCGAGTACAATCN:CGAGTATACAACN
GAGCATTACATGN:AAGCGTACATTGN
CAATATTCAATAN:TCAAGATCAAGAN
CAATATTCAATAN:CTAATATTTGAAN
AGACAAGCTTCCN:GCAAGCTGTCTCN
ATGCAACTCGAAN:TGCAACTTGCAGN
GTCTATACATATN:GCCTTACGATAGN
CTCAGGAGACTTN:CCAGGGACTTCTN
TCATGTGAACGAN:TCAATGACCGCAN
TCATGTGAACGAN:TCAAGATCAAGAN
ACAATCCCGAGTN:TATAATCCGAGGN
GTTCCCAACGGTN:GTGTGCTAACGTN
TCTGATCGAGGTN:TATAATCCGAGGN
Read names are same: 1
1000000
2000000
3000000
4000000
5000000
6000000
7000000
8000000
9000000
10000000
11000000
12000000
13000000
14000000
Done matching barcodes
0 GCTTATTGCTTAN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Bel_CON3037_B.fastq.gz
1 GACCATGTAGTAN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Spr_CON3017_B.fastq.gz
2 CTTCGCGGATGTN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Sla_IPM2070_B.fastq.gz
3 TGAGCGCACGCGN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Dal_CF1051_B.fastq.gz
4 CATGAGACTGTAN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Sum_CF4005_B.fastq.gz
5 TTACCCGCACAGN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Bel_CF3045_A.fastq.gz
6 AAGATTTGCAGCN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Sla_CON2061_A.fastq.gz
7 AACCGATGTACCN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Ber_CF2006_A.fastq.gz
8 GCCTTACGATAGN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Dal_CON1057_A.fastq.gz
9 ACGACCTACGCTN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Bel_Control_A.fastq.gz
10 ATGGCCTGACTAN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Bel_CON3039_B.fastq.gz
11 GCAAGCTGTCTCN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Spr_CON3019_Be2.fastq.gz
12 ATCACATTCTCCN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Sla_IPM2071_B.fastq.gz
13 CGAGTATACAACN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Dal_CF1052_B.fastq.gz
14 CCAGGGACTTCTN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Sum_CF4006_B.fastq.gz
15 ACAAGTGCTGCTN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Bel_CF3047_A.fastq.gz
16 CACTCTCCGGCAN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Sla_CON2063_A.fastq.gz
17 ATTAATGAAGCGN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Ber_CF2007_A.fastq.gz
18 ACCGATTAGGTAN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Dal_CON1058_A.fastq.gz
19 ATCGATCCACAGN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Spr_Control_A.fastq.gz
20 TCAATGACCGCAN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Bel_IPM3042_B.fastq.gz
21 TATCTTCCTGAAN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Spr_IPM3023_B.fastq.gz
22 AACGTCCTGTGCN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Ber_IPM2001_B.fastq.gz
23 TAAGCGTCTCGAN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Dal_IPM1054_B.fastq.gz
24 GAGGTATTCTGAN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Sum_CON4010_B.fastq.gz
25 CGTAAGATGCCTN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Spr_CF3013_A.fastq.gz
26 GGAGGGTACCGTN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Sla_CF2065_A.fastq.gz
27 TCAAGATCAAGAN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Ber_CON2010_A.fastq.gz
28 TGCAACTTGCAGN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Sum_IPM4001_A.fastq.gz
29 TACTAGATATTAN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Sla_Control_A.fastq.gz
30 CTTTATGTGTCAN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Bel_IPM3044_B.fastq.gz
31 GGTACTGTACCAN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Spr_IPM3024_B.fastq.gz
32 AAGGTGGACAAGN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Ber_IPM2002_B.fastq.gz
33 ACGCTCCCATCGN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Dal_IPM1055_B.fastq.gz
34 AGAGCTCCTCTGN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Sum_CON4011_B.fastq.gz
35 GCGTACGGGTGAN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Spr_CF3016_A.fastq.gz
36 AAGCGTACATTGN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Sla_CF2066_A.fastq.gz
37 CTGTTACAGCGAN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Ber_CON2011_A.fastq.gz
38 CCGAGTACAATCN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Sum_IPM4002_A.fastq.gz
39 GGTCTCCTACAGN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Ber_Control_A.fastq.gz
40 GGTCGAATTGCTN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Bel_CF3045_B.fastq.gz
41 TCAACTATGTCTN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Sla_CON2061_B.fastq.gz
42 TATAGAAGAATGN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Ber_CF2006_B.fastq.gz
43 CTAATATTTGAAN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Dal_CON1057_B.fastq.gz
44 GAGCATTACATGN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Bel_CON3037_A.fastq.gz
45 ATATACCTGCGGN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Spr_CON3017_A.fastq.gz
46 CAATATTCAATAN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Sla_IPM2070_A.fastq.gz
47 AAGTGCTTGGTAN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Dal_CF1051_A.fastq.gz
48 GCGGAGCACGTCN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Sum_CF4005_A.fastq.gz
49 TCCCGCCTACGCN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Dal_Control_A.fastq.gz
50 TTACCACATCTAN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Bel_CF3047_B.fastq.gz
51 TGGCATGTTGGTN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Sla_CON2063_B.fastq.gz
52 GTGTGCTAACGTN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Ber_CF2007_B.fastq.gz
53 TGAGTTCGGTCCN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Dal_CON1058_B.fastq.gz
54 AGACAAGCTTCCN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Bel_CON3039_A.fastq.gz
55 TATAATCCGAGGN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Spr_CON3019_A.fastq.gz
56 ATAAAGAGGAGGN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Sla_IPM2071_A.fastq.gz
57 AGTTTGCGAGATN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Dal_CF1052_A.fastq.gz
58 AAGCTAAAGCTAN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Sum_CF4006_A.fastq.gz
59 ACCCTGGGTATCN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Sum_Control_A1.fastq.gz
60 ATGCAACTCGAAN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Spr_CF3013_B.fastq.gz
61 ATCATCTCGGCGN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Sla_CF2065_B.fastq.gz
62 GTCTATACATATN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Ber_CON2010_B.fastq.gz
63 CTCAGGAGACTTN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Sum_IPM4001_B.fastq.gz
64 CATCCTGAGCAAN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Bel_IPM3042_A.fastq.gz
65 GTGACTAGTGATN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Spr_IPM3023_A.fastq.gz
66 TCATGTGAACGAN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Ber_IPM2001_A.fastq.gz
67 CACTTGCTCTCTN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Dal_IPM1054_A.fastq.gz
68 ACAATCCCGAGTN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Sum_CON4010_A.fastq.gz
69 GTTCCCAACGGTN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Dilution.fastq.gz
71 TTGGTGCCTGTGN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Spr_CF3016_B.fastq.gz
72 ATTGGGACATAAN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Sla_CF2066_B.fastq.gz
73 AGTTCGGCATTGN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Ber_CON2011_Be2.fastq.gz
74 TCTGATCGAGGTN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Sum_IPM4002_B.fastq.gz
75 GAATGACGTTTGN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Bel_IPM3044_A.fastq.gz
76 GAAGGAAAGTAGN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Spr_IPM3024_A.fastq.gz
77 AACTGGAACCCTN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Ber_IPM2002_A.fastq.gz
78 AGGAATACTCACN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Dal_IPM1055_A.fastq.gz
79 CCATCGACGCTCN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_Sum_CON4011_A.fastq.gz
80 GTCACCAATCCGN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_NTC.fastq.gz
81 undecoded /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R1_001.fastq.gz_unsigned.fastq.gz
1000000
2000000
3000000
4000000
5000000
6000000
7000000
8000000
9000000
10000000
11000000
12000000
13000000
14000000
0 GCTTATTGCTTAN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Bel_CON3037_B.fastq.gz
1 GACCATGTAGTAN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Spr_CON3017_B.fastq.gz
2 CTTCGCGGATGTN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Sla_IPM2070_B.fastq.gz
3 TGAGCGCACGCGN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Dal_CF1051_B.fastq.gz
4 CATGAGACTGTAN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Sum_CF4005_B.fastq.gz
5 TTACCCGCACAGN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Bel_CF3045_A.fastq.gz
6 AAGATTTGCAGCN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Sla_CON2061_A.fastq.gz
7 AACCGATGTACCN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Ber_CF2006_A.fastq.gz
8 GCCTTACGATAGN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Dal_CON1057_A.fastq.gz
9 ACGACCTACGCTN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Bel_Control_A.fastq.gz
10 ATGGCCTGACTAN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Bel_CON3039_B.fastq.gz
11 GCAAGCTGTCTCN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Spr_CON3019_Be2.fastq.gz
12 ATCACATTCTCCN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Sla_IPM2071_B.fastq.gz
13 CGAGTATACAACN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Dal_CF1052_B.fastq.gz
14 CCAGGGACTTCTN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Sum_CF4006_B.fastq.gz
15 ACAAGTGCTGCTN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Bel_CF3047_A.fastq.gz
16 CACTCTCCGGCAN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Sla_CON2063_A.fastq.gz
17 ATTAATGAAGCGN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Ber_CF2007_A.fastq.gz
18 ACCGATTAGGTAN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Dal_CON1058_A.fastq.gz
19 ATCGATCCACAGN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Spr_Control_A.fastq.gz
20 TCAATGACCGCAN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Bel_IPM3042_B.fastq.gz
21 TATCTTCCTGAAN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Spr_IPM3023_B.fastq.gz
22 AACGTCCTGTGCN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Ber_IPM2001_B.fastq.gz
23 TAAGCGTCTCGAN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Dal_IPM1054_B.fastq.gz
24 GAGGTATTCTGAN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Sum_CON4010_B.fastq.gz
25 CGTAAGATGCCTN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Spr_CF3013_A.fastq.gz
26 GGAGGGTACCGTN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Sla_CF2065_A.fastq.gz
27 TCAAGATCAAGAN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Ber_CON2010_A.fastq.gz
28 TGCAACTTGCAGN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Sum_IPM4001_A.fastq.gz
29 TACTAGATATTAN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Sla_Control_A.fastq.gz
30 CTTTATGTGTCAN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Bel_IPM3044_B.fastq.gz
31 GGTACTGTACCAN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Spr_IPM3024_B.fastq.gz
32 AAGGTGGACAAGN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Ber_IPM2002_B.fastq.gz
33 ACGCTCCCATCGN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Dal_IPM1055_B.fastq.gz
34 AGAGCTCCTCTGN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Sum_CON4011_B.fastq.gz
35 GCGTACGGGTGAN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Spr_CF3016_A.fastq.gz
36 AAGCGTACATTGN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Sla_CF2066_A.fastq.gz
37 CTGTTACAGCGAN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Ber_CON2011_A.fastq.gz
38 CCGAGTACAATCN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Sum_IPM4002_A.fastq.gz
39 GGTCTCCTACAGN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Ber_Control_A.fastq.gz
40 GGTCGAATTGCTN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Bel_CF3045_B.fastq.gz
41 TCAACTATGTCTN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Sla_CON2061_B.fastq.gz
42 TATAGAAGAATGN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Ber_CF2006_B.fastq.gz
43 CTAATATTTGAAN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Dal_CON1057_B.fastq.gz
44 GAGCATTACATGN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Bel_CON3037_A.fastq.gz
45 ATATACCTGCGGN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Spr_CON3017_A.fastq.gz
46 CAATATTCAATAN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Sla_IPM2070_A.fastq.gz
47 AAGTGCTTGGTAN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Dal_CF1051_A.fastq.gz
48 GCGGAGCACGTCN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Sum_CF4005_A.fastq.gz
49 TCCCGCCTACGCN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Dal_Control_A.fastq.gz
50 TTACCACATCTAN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Bel_CF3047_B.fastq.gz
51 TGGCATGTTGGTN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Sla_CON2063_B.fastq.gz
52 GTGTGCTAACGTN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Ber_CF2007_B.fastq.gz
53 TGAGTTCGGTCCN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Dal_CON1058_B.fastq.gz
54 AGACAAGCTTCCN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Bel_CON3039_A.fastq.gz
55 TATAATCCGAGGN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Spr_CON3019_A.fastq.gz
56 ATAAAGAGGAGGN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Sla_IPM2071_A.fastq.gz
57 AGTTTGCGAGATN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Dal_CF1052_A.fastq.gz
58 AAGCTAAAGCTAN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Sum_CF4006_A.fastq.gz
59 ACCCTGGGTATCN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Sum_Control_A1.fastq.gz
60 ATGCAACTCGAAN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Spr_CF3013_B.fastq.gz
61 ATCATCTCGGCGN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Sla_CF2065_B.fastq.gz
62 GTCTATACATATN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Ber_CON2010_B.fastq.gz
63 CTCAGGAGACTTN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Sum_IPM4001_B.fastq.gz
64 CATCCTGAGCAAN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Bel_IPM3042_A.fastq.gz
65 GTGACTAGTGATN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Spr_IPM3023_A.fastq.gz
66 TCATGTGAACGAN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Ber_IPM2001_A.fastq.gz
67 CACTTGCTCTCTN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Dal_IPM1054_A.fastq.gz
68 ACAATCCCGAGTN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Sum_CON4010_A.fastq.gz
69 GTTCCCAACGGTN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Dilution.fastq.gz
71 TTGGTGCCTGTGN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Spr_CF3016_B.fastq.gz
72 ATTGGGACATAAN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Sla_CF2066_B.fastq.gz
73 AGTTCGGCATTGN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Ber_CON2011_Be2.fastq.gz
74 TCTGATCGAGGTN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Sum_IPM4002_B.fastq.gz
75 GAATGACGTTTGN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Bel_IPM3044_A.fastq.gz
76 GAAGGAAAGTAGN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Spr_IPM3024_A.fastq.gz
77 AACTGGAACCCTN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Ber_IPM2002_A.fastq.gz
78 AGGAATACTCACN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Dal_IPM1055_A.fastq.gz
79 CCATCGACGCTCN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_Sum_CON4011_A.fastq.gz
80 GTCACCAATCCGN /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_NTC.fastq.gz
81 undecoded /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/Undetermined_S0_L001_R2_001.fastq.gz_unsigned.fastq.gz
1000000
2000000
3000000
4000000
5000000
6000000
7000000
8000000
9000000
10000000
11000000
12000000
13000000
14000000
list.files(demultiplex.fp)
[1] "Undetermined_S0_L001_I1_001.fastq.gz.decode" "Undetermined_S0_L001_I1_001.fastq.gz.decode.stat" "Undetermined_S0_L001_R1_001.fastq.gz_Bel_CF3045_A.fastq.gz"
[4] "Undetermined_S0_L001_R1_001.fastq.gz_Bel_CF3045_B.fastq.gz" "Undetermined_S0_L001_R1_001.fastq.gz_Bel_CF3047_A.fastq.gz" "Undetermined_S0_L001_R1_001.fastq.gz_Bel_CF3047_B.fastq.gz"
[7] "Undetermined_S0_L001_R1_001.fastq.gz_Bel_CON3037_A.fastq.gz" "Undetermined_S0_L001_R1_001.fastq.gz_Bel_CON3037_B.fastq.gz" "Undetermined_S0_L001_R1_001.fastq.gz_Bel_CON3039_A.fastq.gz"
[10] "Undetermined_S0_L001_R1_001.fastq.gz_Bel_CON3039_B.fastq.gz" "Undetermined_S0_L001_R1_001.fastq.gz_Bel_Control_A.fastq.gz" "Undetermined_S0_L001_R1_001.fastq.gz_Bel_IPM3042_A.fastq.gz"
[13] "Undetermined_S0_L001_R1_001.fastq.gz_Bel_IPM3042_B.fastq.gz" "Undetermined_S0_L001_R1_001.fastq.gz_Bel_IPM3044_A.fastq.gz" "Undetermined_S0_L001_R1_001.fastq.gz_Bel_IPM3044_B.fastq.gz"
[16] "Undetermined_S0_L001_R1_001.fastq.gz_Ber_CF2006_A.fastq.gz" "Undetermined_S0_L001_R1_001.fastq.gz_Ber_CF2006_B.fastq.gz" "Undetermined_S0_L001_R1_001.fastq.gz_Ber_CF2007_A.fastq.gz"
[19] "Undetermined_S0_L001_R1_001.fastq.gz_Ber_CF2007_B.fastq.gz" "Undetermined_S0_L001_R1_001.fastq.gz_Ber_CON2010_A.fastq.gz" "Undetermined_S0_L001_R1_001.fastq.gz_Ber_CON2010_B.fastq.gz"
[22] "Undetermined_S0_L001_R1_001.fastq.gz_Ber_CON2011_A.fastq.gz" "Undetermined_S0_L001_R1_001.fastq.gz_Ber_CON2011_Be2.fastq.gz" "Undetermined_S0_L001_R1_001.fastq.gz_Ber_Control_A.fastq.gz"
[25] "Undetermined_S0_L001_R1_001.fastq.gz_Ber_IPM2001_A.fastq.gz" "Undetermined_S0_L001_R1_001.fastq.gz_Ber_IPM2001_B.fastq.gz" "Undetermined_S0_L001_R1_001.fastq.gz_Ber_IPM2002_A.fastq.gz"
[28] "Undetermined_S0_L001_R1_001.fastq.gz_Ber_IPM2002_B.fastq.gz" "Undetermined_S0_L001_R1_001.fastq.gz_Dal_CF1051_A.fastq.gz" "Undetermined_S0_L001_R1_001.fastq.gz_Dal_CF1051_B.fastq.gz"
[31] "Undetermined_S0_L001_R1_001.fastq.gz_Dal_CF1052_A.fastq.gz" "Undetermined_S0_L001_R1_001.fastq.gz_Dal_CF1052_B.fastq.gz" "Undetermined_S0_L001_R1_001.fastq.gz_Dal_CON1057_A.fastq.gz"
[34] "Undetermined_S0_L001_R1_001.fastq.gz_Dal_CON1057_B.fastq.gz" "Undetermined_S0_L001_R1_001.fastq.gz_Dal_CON1058_A.fastq.gz" "Undetermined_S0_L001_R1_001.fastq.gz_Dal_CON1058_B.fastq.gz"
[37] "Undetermined_S0_L001_R1_001.fastq.gz_Dal_Control_A.fastq.gz" "Undetermined_S0_L001_R1_001.fastq.gz_Dal_IPM1054_A.fastq.gz" "Undetermined_S0_L001_R1_001.fastq.gz_Dal_IPM1054_B.fastq.gz"
[40] "Undetermined_S0_L001_R1_001.fastq.gz_Dal_IPM1055_A.fastq.gz" "Undetermined_S0_L001_R1_001.fastq.gz_Dal_IPM1055_B.fastq.gz" "Undetermined_S0_L001_R1_001.fastq.gz_Dilution.fastq.gz"
[43] "Undetermined_S0_L001_R1_001.fastq.gz_NTC.fastq.gz" "Undetermined_S0_L001_R1_001.fastq.gz_Sla_CF2065_A.fastq.gz" "Undetermined_S0_L001_R1_001.fastq.gz_Sla_CF2065_B.fastq.gz"
[46] "Undetermined_S0_L001_R1_001.fastq.gz_Sla_CF2066_A.fastq.gz" "Undetermined_S0_L001_R1_001.fastq.gz_Sla_CF2066_B.fastq.gz" "Undetermined_S0_L001_R1_001.fastq.gz_Sla_CON2061_A.fastq.gz"
[49] "Undetermined_S0_L001_R1_001.fastq.gz_Sla_CON2061_B.fastq.gz" "Undetermined_S0_L001_R1_001.fastq.gz_Sla_CON2063_A.fastq.gz" "Undetermined_S0_L001_R1_001.fastq.gz_Sla_CON2063_B.fastq.gz"
[52] "Undetermined_S0_L001_R1_001.fastq.gz_Sla_Control_A.fastq.gz" "Undetermined_S0_L001_R1_001.fastq.gz_Sla_IPM2070_A.fastq.gz" "Undetermined_S0_L001_R1_001.fastq.gz_Sla_IPM2070_B.fastq.gz"
[55] "Undetermined_S0_L001_R1_001.fastq.gz_Sla_IPM2071_A.fastq.gz" "Undetermined_S0_L001_R1_001.fastq.gz_Sla_IPM2071_B.fastq.gz" "Undetermined_S0_L001_R1_001.fastq.gz_Spr_CF3013_A.fastq.gz"
[58] "Undetermined_S0_L001_R1_001.fastq.gz_Spr_CF3013_B.fastq.gz" "Undetermined_S0_L001_R1_001.fastq.gz_Spr_CF3016_A.fastq.gz" "Undetermined_S0_L001_R1_001.fastq.gz_Spr_CF3016_B.fastq.gz"
[61] "Undetermined_S0_L001_R1_001.fastq.gz_Spr_CON3017_A.fastq.gz" "Undetermined_S0_L001_R1_001.fastq.gz_Spr_CON3017_B.fastq.gz" "Undetermined_S0_L001_R1_001.fastq.gz_Spr_CON3019_A.fastq.gz"
[64] "Undetermined_S0_L001_R1_001.fastq.gz_Spr_CON3019_Be2.fastq.gz" "Undetermined_S0_L001_R1_001.fastq.gz_Spr_Control_A.fastq.gz" "Undetermined_S0_L001_R1_001.fastq.gz_Spr_IPM3023_A.fastq.gz"
[67] "Undetermined_S0_L001_R1_001.fastq.gz_Spr_IPM3023_B.fastq.gz" "Undetermined_S0_L001_R1_001.fastq.gz_Spr_IPM3024_A.fastq.gz" "Undetermined_S0_L001_R1_001.fastq.gz_Spr_IPM3024_B.fastq.gz"
[70] "Undetermined_S0_L001_R1_001.fastq.gz_Sum_CF4005_A.fastq.gz" "Undetermined_S0_L001_R1_001.fastq.gz_Sum_CF4005_B.fastq.gz" "Undetermined_S0_L001_R1_001.fastq.gz_Sum_CF4006_A.fastq.gz"
[73] "Undetermined_S0_L001_R1_001.fastq.gz_Sum_CF4006_B.fastq.gz" "Undetermined_S0_L001_R1_001.fastq.gz_Sum_CON4010_A.fastq.gz" "Undetermined_S0_L001_R1_001.fastq.gz_Sum_CON4010_B.fastq.gz"
[76] "Undetermined_S0_L001_R1_001.fastq.gz_Sum_CON4011_A.fastq.gz" "Undetermined_S0_L001_R1_001.fastq.gz_Sum_CON4011_B.fastq.gz" "Undetermined_S0_L001_R1_001.fastq.gz_Sum_Control_A1.fastq.gz"
[79] "Undetermined_S0_L001_R1_001.fastq.gz_Sum_IPM4001_A.fastq.gz" "Undetermined_S0_L001_R1_001.fastq.gz_Sum_IPM4001_B.fastq.gz" "Undetermined_S0_L001_R1_001.fastq.gz_Sum_IPM4002_A.fastq.gz"
[82] "Undetermined_S0_L001_R1_001.fastq.gz_Sum_IPM4002_B.fastq.gz" "Undetermined_S0_L001_R1_001.fastq.gz_unsigned.fastq.gz" "Undetermined_S0_L001_R2_001.fastq.gz_Bel_CF3045_A.fastq.gz"
[85] "Undetermined_S0_L001_R2_001.fastq.gz_Bel_CF3045_B.fastq.gz" "Undetermined_S0_L001_R2_001.fastq.gz_Bel_CF3047_A.fastq.gz" "Undetermined_S0_L001_R2_001.fastq.gz_Bel_CF3047_B.fastq.gz"
[88] "Undetermined_S0_L001_R2_001.fastq.gz_Bel_CON3037_A.fastq.gz" "Undetermined_S0_L001_R2_001.fastq.gz_Bel_CON3037_B.fastq.gz" "Undetermined_S0_L001_R2_001.fastq.gz_Bel_CON3039_A.fastq.gz"
[91] "Undetermined_S0_L001_R2_001.fastq.gz_Bel_CON3039_B.fastq.gz" "Undetermined_S0_L001_R2_001.fastq.gz_Bel_Control_A.fastq.gz" "Undetermined_S0_L001_R2_001.fastq.gz_Bel_IPM3042_A.fastq.gz"
[94] "Undetermined_S0_L001_R2_001.fastq.gz_Bel_IPM3042_B.fastq.gz" "Undetermined_S0_L001_R2_001.fastq.gz_Bel_IPM3044_A.fastq.gz" "Undetermined_S0_L001_R2_001.fastq.gz_Bel_IPM3044_B.fastq.gz"
[97] "Undetermined_S0_L001_R2_001.fastq.gz_Ber_CF2006_A.fastq.gz" "Undetermined_S0_L001_R2_001.fastq.gz_Ber_CF2006_B.fastq.gz" "Undetermined_S0_L001_R2_001.fastq.gz_Ber_CF2007_A.fastq.gz"
[100] "Undetermined_S0_L001_R2_001.fastq.gz_Ber_CF2007_B.fastq.gz" "Undetermined_S0_L001_R2_001.fastq.gz_Ber_CON2010_A.fastq.gz" "Undetermined_S0_L001_R2_001.fastq.gz_Ber_CON2010_B.fastq.gz"
[103] "Undetermined_S0_L001_R2_001.fastq.gz_Ber_CON2011_A.fastq.gz" "Undetermined_S0_L001_R2_001.fastq.gz_Ber_CON2011_Be2.fastq.gz" "Undetermined_S0_L001_R2_001.fastq.gz_Ber_Control_A.fastq.gz"
[106] "Undetermined_S0_L001_R2_001.fastq.gz_Ber_IPM2001_A.fastq.gz" "Undetermined_S0_L001_R2_001.fastq.gz_Ber_IPM2001_B.fastq.gz" "Undetermined_S0_L001_R2_001.fastq.gz_Ber_IPM2002_A.fastq.gz"
[109] "Undetermined_S0_L001_R2_001.fastq.gz_Ber_IPM2002_B.fastq.gz" "Undetermined_S0_L001_R2_001.fastq.gz_Dal_CF1051_A.fastq.gz" "Undetermined_S0_L001_R2_001.fastq.gz_Dal_CF1051_B.fastq.gz"
[112] "Undetermined_S0_L001_R2_001.fastq.gz_Dal_CF1052_A.fastq.gz" "Undetermined_S0_L001_R2_001.fastq.gz_Dal_CF1052_B.fastq.gz" "Undetermined_S0_L001_R2_001.fastq.gz_Dal_CON1057_A.fastq.gz"
[115] "Undetermined_S0_L001_R2_001.fastq.gz_Dal_CON1057_B.fastq.gz" "Undetermined_S0_L001_R2_001.fastq.gz_Dal_CON1058_A.fastq.gz" "Undetermined_S0_L001_R2_001.fastq.gz_Dal_CON1058_B.fastq.gz"
[118] "Undetermined_S0_L001_R2_001.fastq.gz_Dal_Control_A.fastq.gz" "Undetermined_S0_L001_R2_001.fastq.gz_Dal_IPM1054_A.fastq.gz" "Undetermined_S0_L001_R2_001.fastq.gz_Dal_IPM1054_B.fastq.gz"
[121] "Undetermined_S0_L001_R2_001.fastq.gz_Dal_IPM1055_A.fastq.gz" "Undetermined_S0_L001_R2_001.fastq.gz_Dal_IPM1055_B.fastq.gz" "Undetermined_S0_L001_R2_001.fastq.gz_Dilution.fastq.gz"
[124] "Undetermined_S0_L001_R2_001.fastq.gz_NTC.fastq.gz" "Undetermined_S0_L001_R2_001.fastq.gz_Sla_CF2065_A.fastq.gz" "Undetermined_S0_L001_R2_001.fastq.gz_Sla_CF2065_B.fastq.gz"
[127] "Undetermined_S0_L001_R2_001.fastq.gz_Sla_CF2066_A.fastq.gz" "Undetermined_S0_L001_R2_001.fastq.gz_Sla_CF2066_B.fastq.gz" "Undetermined_S0_L001_R2_001.fastq.gz_Sla_CON2061_A.fastq.gz"
[130] "Undetermined_S0_L001_R2_001.fastq.gz_Sla_CON2061_B.fastq.gz" "Undetermined_S0_L001_R2_001.fastq.gz_Sla_CON2063_A.fastq.gz" "Undetermined_S0_L001_R2_001.fastq.gz_Sla_CON2063_B.fastq.gz"
[133] "Undetermined_S0_L001_R2_001.fastq.gz_Sla_Control_A.fastq.gz" "Undetermined_S0_L001_R2_001.fastq.gz_Sla_IPM2070_A.fastq.gz" "Undetermined_S0_L001_R2_001.fastq.gz_Sla_IPM2070_B.fastq.gz"
[136] "Undetermined_S0_L001_R2_001.fastq.gz_Sla_IPM2071_A.fastq.gz" "Undetermined_S0_L001_R2_001.fastq.gz_Sla_IPM2071_B.fastq.gz" "Undetermined_S0_L001_R2_001.fastq.gz_Spr_CF3013_A.fastq.gz"
[139] "Undetermined_S0_L001_R2_001.fastq.gz_Spr_CF3013_B.fastq.gz" "Undetermined_S0_L001_R2_001.fastq.gz_Spr_CF3016_A.fastq.gz" "Undetermined_S0_L001_R2_001.fastq.gz_Spr_CF3016_B.fastq.gz"
[142] "Undetermined_S0_L001_R2_001.fastq.gz_Spr_CON3017_A.fastq.gz" "Undetermined_S0_L001_R2_001.fastq.gz_Spr_CON3017_B.fastq.gz" "Undetermined_S0_L001_R2_001.fastq.gz_Spr_CON3019_A.fastq.gz"
[145] "Undetermined_S0_L001_R2_001.fastq.gz_Spr_CON3019_Be2.fastq.gz" "Undetermined_S0_L001_R2_001.fastq.gz_Spr_Control_A.fastq.gz" "Undetermined_S0_L001_R2_001.fastq.gz_Spr_IPM3023_A.fastq.gz"
[148] "Undetermined_S0_L001_R2_001.fastq.gz_Spr_IPM3023_B.fastq.gz" "Undetermined_S0_L001_R2_001.fastq.gz_Spr_IPM3024_A.fastq.gz" "Undetermined_S0_L001_R2_001.fastq.gz_Spr_IPM3024_B.fastq.gz"
[151] "Undetermined_S0_L001_R2_001.fastq.gz_Sum_CF4005_A.fastq.gz" "Undetermined_S0_L001_R2_001.fastq.gz_Sum_CF4005_B.fastq.gz" "Undetermined_S0_L001_R2_001.fastq.gz_Sum_CF4006_A.fastq.gz"
[154] "Undetermined_S0_L001_R2_001.fastq.gz_Sum_CF4006_B.fastq.gz" "Undetermined_S0_L001_R2_001.fastq.gz_Sum_CON4010_A.fastq.gz" "Undetermined_S0_L001_R2_001.fastq.gz_Sum_CON4010_B.fastq.gz"
[157] "Undetermined_S0_L001_R2_001.fastq.gz_Sum_CON4011_A.fastq.gz" "Undetermined_S0_L001_R2_001.fastq.gz_Sum_CON4011_B.fastq.gz" "Undetermined_S0_L001_R2_001.fastq.gz_Sum_Control_A1.fastq.gz"
[160] "Undetermined_S0_L001_R2_001.fastq.gz_Sum_IPM4001_A.fastq.gz" "Undetermined_S0_L001_R2_001.fastq.gz_Sum_IPM4001_B.fastq.gz" "Undetermined_S0_L001_R2_001.fastq.gz_Sum_IPM4002_A.fastq.gz"
[163] "Undetermined_S0_L001_R2_001.fastq.gz_Sum_IPM4002_B.fastq.gz" "Undetermined_S0_L001_R2_001.fastq.gz_unsigned.fastq.gz"
fnRs
[1] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Bel_CF3045_A.fastq.gz"
[2] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Bel_CF3045_B.fastq.gz"
[3] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Bel_CF3047_A.fastq.gz"
[4] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Bel_CF3047_B.fastq.gz"
[5] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Bel_CON3037_A.fastq.gz"
[6] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Bel_CON3037_B.fastq.gz"
[7] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Bel_CON3039_A.fastq.gz"
[8] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Bel_CON3039_B.fastq.gz"
[9] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Bel_Control_A.fastq.gz"
[10] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Bel_IPM3042_A.fastq.gz"
[11] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Bel_IPM3042_B.fastq.gz"
[12] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Bel_IPM3044_A.fastq.gz"
[13] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Bel_IPM3044_B.fastq.gz"
[14] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Ber_CF2006_A.fastq.gz"
[15] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Ber_CF2006_B.fastq.gz"
[16] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Ber_CF2007_A.fastq.gz"
[17] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Ber_CF2007_B.fastq.gz"
[18] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Ber_CON2010_A.fastq.gz"
[19] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Ber_CON2010_B.fastq.gz"
[20] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Ber_CON2011_A.fastq.gz"
[21] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Ber_CON2011_Be2.fastq.gz"
[22] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Ber_Control_A.fastq.gz"
[23] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Ber_IPM2001_A.fastq.gz"
[24] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Ber_IPM2001_B.fastq.gz"
[25] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Ber_IPM2002_A.fastq.gz"
[26] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Ber_IPM2002_B.fastq.gz"
[27] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Dal_CF1051_A.fastq.gz"
[28] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Dal_CF1051_B.fastq.gz"
[29] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Dal_CF1052_A.fastq.gz"
[30] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Dal_CF1052_B.fastq.gz"
[31] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Dal_CON1057_A.fastq.gz"
[32] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Dal_CON1057_B.fastq.gz"
[33] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Dal_CON1058_A.fastq.gz"
[34] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Dal_CON1058_B.fastq.gz"
[35] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Dal_Control_A.fastq.gz"
[36] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Dal_IPM1054_A.fastq.gz"
[37] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Dal_IPM1054_B.fastq.gz"
[38] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Dal_IPM1055_A.fastq.gz"
[39] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Dal_IPM1055_B.fastq.gz"
[40] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Dilution.fastq.gz"
[41] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_NTC.fastq.gz"
[42] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Sla_CF2065_A.fastq.gz"
[43] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Sla_CF2065_B.fastq.gz"
[44] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Sla_CF2066_A.fastq.gz"
[45] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Sla_CF2066_B.fastq.gz"
[46] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Sla_CON2061_A.fastq.gz"
[47] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Sla_CON2061_B.fastq.gz"
[48] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Sla_CON2063_A.fastq.gz"
[49] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Sla_CON2063_B.fastq.gz"
[50] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Sla_Control_A.fastq.gz"
[51] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Sla_IPM2070_A.fastq.gz"
[52] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Sla_IPM2070_B.fastq.gz"
[53] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Sla_IPM2071_A.fastq.gz"
[54] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Sla_IPM2071_B.fastq.gz"
[55] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Spr_CF3013_A.fastq.gz"
[56] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Spr_CF3013_B.fastq.gz"
[57] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Spr_CF3016_A.fastq.gz"
[58] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Spr_CF3016_B.fastq.gz"
[59] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Spr_CON3017_A.fastq.gz"
[60] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Spr_CON3017_B.fastq.gz"
[61] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Spr_CON3019_A.fastq.gz"
[62] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Spr_CON3019_Be2.fastq.gz"
[63] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Spr_Control_A.fastq.gz"
[64] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Spr_IPM3023_A.fastq.gz"
[65] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Spr_IPM3023_B.fastq.gz"
[66] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Spr_IPM3024_A.fastq.gz"
[67] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Spr_IPM3024_B.fastq.gz"
[68] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Sum_CF4005_A.fastq.gz"
[69] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Sum_CF4005_B.fastq.gz"
[70] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Sum_CF4006_A.fastq.gz"
[71] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Sum_CF4006_B.fastq.gz"
[72] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Sum_CON4010_A.fastq.gz"
[73] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Sum_CON4010_B.fastq.gz"
[74] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Sum_CON4011_A.fastq.gz"
[75] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Sum_CON4011_B.fastq.gz"
[76] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Sum_Control_A1.fastq.gz"
[77] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Sum_IPM4001_A.fastq.gz"
[78] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Sum_IPM4001_B.fastq.gz"
[79] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Sum_IPM4002_A.fastq.gz"
[80] "/Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/demultiplexed/R2_Sum_IPM4002_B.fastq.gz"
# Name the N-filtered files to put them in filtN/ subdirectory
fnFs.filtN <- file.path(preprocess.fp, "filtN", basename(fnFs))
fnRs.filtN <- file.path(preprocess.fp, "filtN", basename(fnRs))
# Filter Ns from reads and put them into the filtN directory
filterAndTrim(fnFs, fnFs.filtN, fnRs, fnRs.filtN, maxN = 0, multithread = TRUE)
Creating output directory: /Users/gordoncuster/Desktop/Quick_Sync/Lopez_Uribe/01_preprocess/filtN
# CHANGE multithread to FALSE on Windows (here and elsewhere in the program)
# Set up the primer sequences to pass along to cutadapt
FWD <- "GTGYCAGCMGCCGCGGTAA" ## this is 515f
REV <- "GGACTACNVGGGTWTCTAAT" ## this is 806Br
# Write a function that creates a list of all orientations of the primers
allOrients <- function(primer) {
# Create all orientations of the input sequence
require(Biostrings)
dna <- DNAString(primer) # The Biostrings works w/ DNAString objects rather than character vectors
orients <- c(Forward = dna, Complement = complement(dna), Reverse = reverse(dna),
RevComp = reverseComplement(dna))
return(sapply(orients, toString)) # Convert back to character vector
}
# Save the primer orientations to pass to cutadapt
FWD.orients <- allOrients(FWD)
REV.orients <- allOrients(REV)
FWD.orients
Forward Complement Reverse RevComp
"GTGYCAGCMGCCGCGGTAA" "CACRGTCGKCGGCGCCATT" "AATGGCGCCGMCGACYGTG" "TTACCGCGGCKGCTGRCAC"
## Forward Complement Reverse
## "GTGYCAGCMGCCGCGGTAA" "CACRGTCGKCGGCGCCATT" "AATGGCGCCGMCGACYGTG"
## RevComp
## "TTACCGCGGCKGCTGRCAC"
# Write a function that counts how many time primers appear in a sequence
primerHits <- function(primer, fn) {
# Counts number of reads in which the primer is found
nhits <- vcountPattern(primer, sread(readFastq(fn)), fixed = FALSE)
return(sum(nhits > 0))
}
rbind(FWD.ForwardReads = sapply(FWD.orients, primerHits, fn = fnFs.filtN[[1]]),
FWD.ReverseReads = sapply(FWD.orients, primerHits, fn = fnRs.filtN[[1]]),
REV.ForwardReads = sapply(REV.orients, primerHits, fn = fnFs.filtN[[1]]),
REV.ReverseReads = sapply(REV.orients, primerHits, fn = fnRs.filtN[[1]]))
Forward Complement Reverse RevComp
FWD.ForwardReads 0 0 0 0
FWD.ReverseReads 0 0 0 12
REV.ForwardReads 0 0 0 17
REV.ReverseReads 1 0 0 0
## Forward Complement Reverse RevComp
## FWD.ForwardReads 0 0 0 0
## FWD.ReverseReads 0 0 0 12
## REV.ForwardReads 0 0 0 17
## REV.ReverseReads 1 0 0 0
# Create directory to hold the output from cutadapt
if (!dir.exists(trimmed.fp)) dir.create(trimmed.fp)
fnFs.cut <- file.path(trimmed.fp, basename(fnFs))
fnRs.cut <- file.path(trimmed.fp, basename(fnRs))
# Save the reverse complements of the primers to variables
FWD.RC <- dada2:::rc(FWD)
REV.RC <- dada2:::rc(REV)
## Create the cutadapt flags ##
# Trim FWD and the reverse-complement of REV off of R1 (forward reads)
R1.flags <- paste("-g", FWD, "-a", REV.RC, "--minimum-length 50")
# Trim REV and the reverse-complement of FWD off of R2 (reverse reads)
R2.flags <- paste("-G", REV, "-A", FWD.RC, "--minimum-length 50")
# Run Cutadapt
for (i in seq_along(fnFs)) {
system2(cutadapt, args = c(R1.flags, R2.flags, "-n", 2, # -n 2 required to remove FWD and REV from reads
"-o", fnFs.cut[i], "-p", fnRs.cut[i], # output files
fnFs.filtN[i], fnRs.filtN[i])) # input files
}
# As a sanity check, we will check for primers in the first cutadapt-ed sample:
rbind(FWD.ForwardReads = sapply(FWD.orients, primerHits, fn = fnFs.cut[[1]]),
FWD.ReverseReads = sapply(FWD.orients, primerHits, fn = fnRs.cut[[1]]),
REV.ForwardReads = sapply(REV.orients, primerHits, fn = fnFs.cut[[1]]),
REV.ReverseReads = sapply(REV.orients, primerHits, fn = fnRs.cut[[1]]))
## Forward Complement Reverse RevComp
## FWD.ForwardReads 0 0 0 0
## FWD.ReverseReads 0 0 0 0
## REV.ForwardReads 0 0 0 0
## REV.ReverseReads 0 0 0 0
dir.create(filter.fp)
subF.fp <- file.path(filter.fp, "preprocessed_F")
subR.fp <- file.path(filter.fp, "preprocessed_R")
dir.create(subF.fp)
dir.create(subR.fp)
# Move R1 and R2 from trimmed to separate forward/reverse sub-directories
fnFs.Q <- file.path(subF.fp, basename(fnFs))
fnRs.Q <- file.path(subR.fp, basename(fnRs))
file.rename(from = fnFs.cut, to = fnFs.Q)
## [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
## [15] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
## [29] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
## [43] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
## [57] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
## [71] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
file.rename(from = fnRs.cut, to = fnRs.Q)
## [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
## [15] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
## [29] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
## [43] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
## [57] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
## [71] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
# File parsing; create file names and make sure that forward and reverse files match
filtpathF <- file.path(subF.fp, "filtered") # files go into preprocessed_F/filtered/
filtpathR <- file.path(subR.fp, "filtered") # ...
fastqFs <- sort(list.files(subF.fp, pattern="fastq.gz"))
fastqRs <- sort(list.files(subR.fp, pattern="fastq.gz"))
if(length(fastqFs) != length(fastqRs)) stop("Forward and reverse files do not match.")
ggplotly(fwd_qual_plots)
ggplotly(rev_qual_plots)